[BioC] Dist of exprSet object
Francois Pepin
fpepin at cs.mcgill.ca
Thu Jul 27 20:10:04 CEST 2006
Hi Marco,
you made a little typo, the function is rowMeans, not rawMeans.
Francois
On Thu, 2006-07-27 at 10:54 -0700, Marco Blanchette wrote:
> Can't find any info on rawMeans:
>
> > ?rawMeans
> No documentation for 'rawMeans' in specified packages and libraries:
> you could try 'help.search("rawMeans")'
>
>
> On 7/27/06 2:00 AM, "Wolfgang Huber" <huber at ebi.ac.uk> wrote:
>
> > Hi Marco,
> >
> > 1) have a look at "rowMeans"
> >
> > 2) have a look at the functions "cut" and "split"
> >
> > x = rnorm(100)
> > ct = cut(rank(x), 10)
> > sp = split(x, ct)
> > boxplot(sp)
> >
> >
> > Cheers
> > Wolfgang
> >
> >> Hum... This exemplified my hate-love relationship that I have with R... Very
> >> powerful, but very difficult to master...
> >>
> >> One more issue. Each experiments are in duplicates (2 experiments, 2
> >> replicates -> 4 arrays). My goal is to partition the distribution in genes
> >> in the 10% top most expressed, 10% to 20% most expressed, 20% to 30% most
> >> expressed, and so on.
> >>
> >> eset is my exprSet object containing the rma computed expression for each
> >> gene on the 4 arrays:
> >>> eset
> >> Expression Set (exprSet) with
> >> 18952 genes
> >> 4 samples
> >> phenoData object with 1 variables and 4 cases
> >> varLabels
> >> sample: arbitrary numbering
> >>
> >> So I need to:
> >>
> >> 1) Get the average expression for each gene from the 2 replicates
> >> Would you do:
> >>> exp1 = iter(eset[,1,2], , mean)
> >>> exp2 = iter(eset[,2,3], , mean)
> >>
> >> Or is there a better way?
> >>
> >> 2) Break down the distribution per 10% bin as in
> >>> top10 = geneNames(eset)[(rank(exp1) >= 0*(length(exp1)/10) & rank(exp1) <
> >> 1*(length(exp1)/10))]
> >>> top10_20 = geneNames(eset)[(rank(exp1) >= 1*(length(exp1)/10) & rank(exp1) <
> >> 2*(length(exp1)/10))]
> >> top20_30 = geneNames(eset)[(rank(exp1) >= 2*(length(exp1)/10) & rank(exp1) <
> >> 3*(length(exp1)/10))]
> >>
> >> Or is there a better way? [I'm pretty sure there a more R elegant way than
> >> that...]
> >>
> >> Many thanks folks
> >>
> >> Cheers,
> >>
> >> Marco
> >>
> >>
> >> On 7/26/06 4:05 PM, "Ben Bolstad" <bmb at bmbolstad.com> wrote:
> >>
> >>> Actually you need affyPLM loaded to boxplot an exprSet. affy only
> >>> provides the method for AffyBatch objects. Otherwise your example is
> >>> correct.
> >>>
> >>> Best,
> >>>
> >>> Ben
> >>>
> >>>
> >>> eg .....
> >>>
> >>>> library(affy)
> >>> Loading required package: Biobase
> >>> Loading required package: tools
> >>>
> >>> Welcome to Bioconductor
> >>>
> >>>
> >>> Vignettes contain introductory material.
> >>>
> >>> To view, simply type 'openVignette()' or start with 'help(Biobase)'.
> >>>
> >>> For details on reading vignettes, see the openVignette help page.
> >>>
> >>>
> >>> Loading required package: affyio
> >>>> library(affydata)
> >>>> data(Dilution)
> >>>> eset <- rma(Dilution)
> >>> Background correcting
> >>> Normalizing
> >>> Calculating Expression
> >>>> boxplot(eset) # throws error
> >>> Error in boxplot.default(eset) : invalid first argument
> >>>> library(affyPLM)
> >>> Loading required package: gcrma
> >>> Loading required package: matchprobes
> >>>> boxplot(eset) #works fine.
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> On Thu, 2006-07-27 at 10:58 +1200, Marcus Davy wrote:
> >>>> P 17 of the vignette("affy").
> >>>>
> >>>> e.g.
> >>>>
> >>>> chipCols <- rainbow(ncol(exprs(affybatch.example)))
> >>>> boxplot(affybatch.example, col=chipCols)
> >>>>
> >>>> Marcus
> >>>>
> >>>>
> >>>> On 7/27/06 10:40 AM, "Marco Blanchette" <mblanche at berkeley.edu> wrote:
> >>>>
> >>>>> Thank you all,
> >>>>>
> >>>>> Using bioclite to download the annotation fixed the problem.
> >>>>>
> >>>>> Now, I am getting into simpler R problem. I have an exprSet object of 4
> >>>>> arrays:
> >>>>>> eset
> >>>>> Expression Set (exprSet) with
> >>>>> 18952 genes
> >>>>> 4 samples
> >>>>> phenoData object with 1 variables and 4 cases
> >>>>> varLabels
> >>>>> sample: arbitrary numbering
> >>>>>
> >>>>> My goal is to draw a boxplot of the 4 different samples. Surely I can do:
> >>>>>> boxplot (exprs(eset)[,1], exprs(eset)[,2], exprs(eset)[,3],
> >>>>>> exprs(eset)[,4],
> >>>>> col=c(2,3,4,5))
> >>>>>
> >>>>> But is there an easier way to do with without having to subscript each
> >>>>> individual column? [right now I have only 4 but when I will have 20, I¹ll
> >>>>> get bored quite rapidly]
> >>>>>
> >>>>> Sorry if this sounds easy, I am still learning the basics of R
> >>>>>
> >>>>> Marco
> >>>>> ______________________________
> >>>>> Marco Blanchette, Ph.D.
> >>>>>
> >>>>> mblanche at uclink.berkeley.edu
> >>>>>
> >>>>> Donald C. Rio's lab
> >>>>> Department of Molecular and Cell Biology
> >>>>> 16 Barker Hall
> >>>>> University of California
> >>>>> Berkeley, CA 94720-3204
> >>>>>
> >>>>> Tel: (510) 642-1084
> >>>>> Cell: (510) 847-0996
> >>>>> Fax: (510) 642-6062
> >>>>
> >>>> ______________________________________________________
> >>>>
> >>>> The contents of this e-mail are privileged and/or confidenti...{{dropped}}
> >>>>
> >>>> _______________________________________________
> >>>> Bioconductor mailing list
> >>>> Bioconductor at stat.math.ethz.ch
> >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >>>> Search the archives:
> >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>
> >> ______________________________
> >> Marco Blanchette, Ph.D.
> >>
> >> mblanche at uclink.berkeley.edu
> >>
> >> Donald C. Rio's lab
> >> Department of Molecular and Cell Biology
> >> 16 Barker Hall
> >> University of California
> >> Berkeley, CA 94720-3204
> >>
> >> Tel: (510) 642-1084
> >> Cell: (510) 847-0996
> >> Fax: (510) 642-6062
> >> --
> >>
> >> _______________________________________________
> >> Bioconductor mailing list
> >> Bioconductor at stat.math.ethz.ch
> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> Search the archives:
> >> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
>
>
> Marco Blanchette, Ph.D.
>
> mblanche at berkeley.edu
>
> Donald C. Rio's lab
> Department of Molecular and Cell Biology
> 16 Barker Hall
> University of California
> Berkeley, CA 94720-3204
>
> Tel: (510) 642-1084
> Cell: (510) 847-0996
> Fax: (510) 642-6062
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>
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